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open-archaeo
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Routines to read and analyze LA-ICP-MS data from the Field Museum's Elemental Analysis Facility LA ICP MS-Routines_FMNH Routines to read and analyze LA-ICP-MS data from the Field Museum's Elemental Analysis Facility Significant contributions include:- Reading in large amounts of cleaned LA-ICP-MS data from xlsx files with each day as a separate sheet- Tidying the LA-ICP-MS data into a tidy data frame- Functions for converting elements calculated as % oxide to ppm- Writing the file to a csv in...
Topics: GitHub, code, software, git
open-archaeo
software

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R-script for conducting and evaluating bootstrapped correspondence analyses following methods published by Peeples and Schachner (2012) in the Journal of Archaeological Science Bootstrap-Correspondence-Analysis R-script for conducting and evaluating bootstrapped correspondence analyses following methods published by Peeples and Schachner (2012) in the Journal of Archaeological Science This code relates to the following article: Peeples, Matthew A. and Gregson Schachner2012 Refining...
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open-archaeo
software

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Script for conducting K-means cluster analysis using R. This script provides output designed to help the user select an appropriate cluster solution. Kmeans Script for conducting K-means cluster analysis using R. This script provides output designed to help the user select an appropriate cluster solution. K-means Cluster Analysis:K-means analysis is a divisive, non-hierarchical method of defining clusters. This is an iterative process, which means that at each step the membership of each...
Topics: GitHub, code, software, git
open-archaeo
software

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A set of GNU Octave functions for biodistance analysis based on non-metric traits To restore the repository download the bundle wget https://archive.org/download/github.com-pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12/pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12.bundle and run: git clone pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12.bundle Source: https://github.com/pr0m1th3as/non-metric-trait-analysis Uploader: pr0m1th3as Upload date: 2018-03-08
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open-archaeo
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R Shiny Document - Visualizing model functions in Neimans 'Stylistic variation in evolutionary perspective' with an interactive document The interactive document neiman1995.Rmd aims to visualize the model functions in Neiman, F. (1995). Stylistic Variation in Evolutionary Perspective: Inferences from Decorative Diversity and Interassemblage Distance in Illinois Woodland Ceramic Assemblages. American Antiquity, 60(1), 7-36. doi:10.2307/282074 For study and teaching purposes. To restore the...
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open-archaeo
software

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This R script produces a exploratory visual for assessing site date ranges originally suggested to me by Wesley Bernardini (Redlands University). The plot consits of horizontal bars on an x-axis reprenting time with the width determined based on the production span for that type and with the height of each box determined based on the relative frequency of that type with types sorted vertically by start date. The script reads in csv files in the formatted of the example dataset here and produces...
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open-archaeo
software

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Dynamic and static 3D plotting for vegan What is vegan3d? vegan3d is an R package of 3D plotting routines split apart from vegan . It can be used for dynamic plots based on rgl package,and for static 3D plots based on scatterplot3d package. The package contains the following functions: ordirgl with its support functions orglpoints , orgltext , orglsegments , orglellipse , orglspider , orglcluster and orglspantree . Theserequire rgl package and provide dynamic ordination graphics.See a simple...
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open-archaeo
by Big-Ancient-Mediterranean
software

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A tool for the geospatial analysis, literary network visualization, and plot mapping of ancient texts To restore the repository download the bundle wget https://archive.org/download/github.com-Big-Ancient-Mediterranean-BAM_-_2018-09-16_12-29-16/Big-Ancient-Mediterranean-BAM_-_2018-09-16_12-29-16.bundle and run: git clone Big-Ancient-Mediterranean-BAM_-_2018-09-16_12-29-16.bundle Source: https://github.com/Big-Ancient-Mediterranean/BAM Uploader: Big-Ancient-Mediterranean Upload date: 2018-09-16
Topics: GitHub, code, software, git
open-archaeo
software

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Element Sourcing in R ElementSourcing Element Sourcing in R This R script is designed to source archaeological artifacts using elemental composition. It is primarily being designed to source obsidian, but I plan to adapt it for broader uses. To restore the repository download the bundle wget https://archive.org/download/github.com-bischrob-ElementSourcing_-_2018-02-06_20-35-44/bischrob-ElementSourcing_-_2018-02-06_20-35-44.bundle and run: git clone...
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open-archaeo
by scollinselliott
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Roman Peasant Project Small Finds Ontology Small Finds from Roman Peasant Project (2009-2014): Technical notes on a behavioral analysis of Roman sites in rural Tuscany. Information may also be found at https://volweb.utk.edu/~scolli46/rppsf.html . The code below depends on the following csv files which contain the semantic graph, as the original graph was composed in Gephi and exported: dataset.csv - table of small finds listed by site, phase, and definition, by count and weight. nodes.csv -...
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open-archaeo
software

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A QGIS plugin to simplfy digitization of archaeological plans drawn using the Museum of London Single Context Recording methodology. ARK Spatial A QGIS plugin for Archaeological Recording.Part of the Archaeological Recording Kit by L-P : Archaeologyhttp://ark.lparchaeology.com Installation Currently ARK Spatial must be manually installed via a Git clone and pb_tool. Clone the repository from GitHub: 'git clone https://github.com/lparchaeology/ArkPlan.git' Initialise the Git submodules: 'cd...
Topics: GitHub, code, software, git
open-archaeo
software

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Script for calculating mean ceramic dates based on tabular data. This script also estimates sampling error using a bootstrapping procedure. Mean-Ceramic-Date-and-Error-Estimation Script for calculating mean ceramic dates based on tabular data. This script also estimates sampling error using a bootstrapping procedure. Mean Ceramic Dates:The mean ceramic date (MCD) of an assemblage is a point estimate of the occupation of a site calculated based on the frequency and date range of types present,...
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open-archaeo
software

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Gianmarco Alberti Miscellaneous GmAMisc (Gianmarco Alberti Miscellaneous) vers 0.24 GmAMisc is a collection of functions that I have built in different points in time. The functions' aim spans from univariate outlier detection, to permutation t test, permutation chi-square test, calculation of Brainerd-Robinson similarity coefficient, validation of logistic regression models, point pattern analysis, and more. The package comes with some toy datasets: assemblage : distribution of 7...
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open-archaeo
software

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The R-script implements a means for statistically assessing the degree of co-occurrence between classes within a dataset based on an idea origially suggested by James Allison at BYU and published by Keith Kintigh in 2006. Binomial-Co-occurrence-Assessment The R-script implements a means for statistically assessing the degree of co-occurrence between classes within a dataset based on an idea origially suggested by James Allison at BYU and published by Keith Kintigh in 2006. I have implemented...
Topics: GitHub, code, software, git
open-archaeo
software

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A directory of GitHub projects by OR for archaeologists Archaeology @ GitHub This is a directory of GitHub projects by OR for archaeologists. Submit pull requests to add new projects. Of course, you can also submit links to git repos elsewhere, or to Mercurial repos, etc. The focus of this directory is not on the software per se , but rather on the fact that git is used to develop and share source code, literate programming resources, archaeological data, etc. Stuff seen at #caasiena (not...
Topics: GitHub, code, software, git
open-archaeo
software

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None R-Scripts This contains a set of data about human mobility, subsistance, population, and environmental productivity derived from the Standard Cross Cultural Sample . Missing cases have been filled in via Multiple Imputation. It also contains a suite of R scripts for processing these data. Included routines are cluster analyses, Multidimentional Scaling, and Canonical Correspondence analysis. Plotting commands are also included. These data and analyses were used in my article "Towards...
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open-archaeo
software

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export of posts from dayofarchaeology.com dayofarchaeology export of posts from dayofarchaeology.com To restore the repository download the bundle wget https://archive.org/download/github.com-drmattlaw-dayofarchaeology_-_2018-09-20_19-17-11/drmattlaw-dayofarchaeology_-_2018-09-20_19-17-11.bundle and run: git clone drmattlaw-dayofarchaeology_-_2018-09-20_19-17-11.bundle Source: https://github.com/drmattlaw/dayofarchaeology Uploader: drmattlaw Upload date: 2018-09-20
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open-archaeo
software

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None arshm-release Experimental mobile app demoing cultural heritage documentation tools in augmented reality. Supports capturing and annotating photos in 3D space. Proof-of-concept features in the app include image anchoring and surface drawing tools. Implemented in Unity using the ARInterface library for cross-platform AR support. Created in Spring 2018 as part of a Computer Science Independent Work project at Princeton University, advised by Professor Branko Glisic and Rebecca Napolitano....
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open-archaeo
software

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for some tools in respect to pollen data processing (you might have guessed). Will turn into a package, maybe. pollen data processing for some tools in respect to pollen data processing (you might have guessed). Will turn into a packet, maybe. To restore the repository download the bundle wget https://archive.org/download/github.com-MartinHinz-pollen_data_processing_-_2018-05-23_12-54-10/MartinHinz-pollen_data_processing_-_2018-05-23_12-54-10.bundle and run: git clone...
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open-archaeo
software

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R Package for contingency tables seriation via Correspondence Analysis CAseriation ver 0.3 CAseriation allows to sort the rows and columns of the input contingency table according to the scores of rows and columns on the Correspondence Analysis' dimension selected by the user. The package also allows to plot the CA scatterplot of selected dimensions, and to seek for clusters in the dataset. As for seriation, two plots are returned, displaying the sorted contingency table. The results are also...
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open-archaeo
software

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None TOPAS - TOolkit for Processing and Annotating Sequence data This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules. Example Invocation: java -jar topas.jar -? This lists all available modules. | FASTA Processing Modules | FASTQ Processing Modules | GFF Processing Modules | VCF Processing Modules || ------------- |...
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open-archaeo
software

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a light-weight database application designed to standardize and simplify data entry of archaeological or historical artifacts. ARCHIE An open source digitial inventory system designed for field and lab use byarchelogists. Branch | Build Status------ | ------------ Master | Development | Contents License Contact Info Dependencies License This Application falls under the Standard GPL v2. See Licence included with this tar file. Credit for code is listed in the changelog, or in the respective...
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open-archaeo
software

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DIYFieldworkDatabase Overview of the system I put together a little DIY fieldwork database server using nearly entirely open source tools and software. It consists of a Raspberry Pi operating on a local network, which contains a MariaDB server, a SMB file sharing server, an R Shiny server, and automatic scheduled backups, but can be configured or extended to suit whatever situation you're in. This is a more collaborative and distributed setup than a typical Microsoft Access setup (or even...
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open-archaeo
software

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Analytical Dashboard for conducting various analysis to group and assess groupings for Neutron Activation Analytical chemical compositional data NAA analytical dashboard Analytical Dashboard for conducting various analysis to group and assess groupings for Neutron Activation Analytical chemical compositional data Very much a work in progress at this point but includes scripts to assess group membership probabilities using Mahalanobis distances (following Neff 2002) and a procedure for selecting...
Topics: GitHub, code, software, git
open-archaeo
software

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An app for use in archaeological field survey to collect high-accurate point locations, photographs, and other data, using affordable differential GNSS equipment. Archaeology Survey - Android App This Android app is designed to support data collection during archaeological fieldwork. Specifically, this app can be modified to fit the data structures and infrastructure of a field surface survey project that involves fieldwalking. The main goal of this app is to geolocate field observations,...
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open-archaeo
software

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Tools to use and manipulate total station data totalstation-tools Tools to use and manipulate total station data Installation Requires a setup with python2.7. You can setup a virtualenv or conda env for this. Clone repository ``` clone repository from Github git clone https://github.com/WiseLabCMU/totalstation-tools.git clone totalopenstation as a submodule (if you do not want to set this up yourself, you should skip the submodule initialization) git submodule update --init``` Install...
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open-archaeo
software

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R Package - Explore SDS datasets (Systematic and digital documentation of stone artefacts) sdsanalysis sdsanalysis is the backbone of the sdsbrowser webapp. To learn more about it's role for this webapp please check the For developers section in the README over there. Beyond that sdsanalysis can be employed to analysis SDS stone artefact data in R. It offers two major functionalities for this purpose: Download available SDS datasets ?sdsdownload sdsanalysis offers functions to access openly...
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open-archaeo
by benmarwick
software

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Scientific Computing Environment for archaeology: Installing R, Rstudio and other things on a lightweight Linux in a VirtualBox virtual machine To restore the repository download the bundle wget https://archive.org/download/gist.github.com-11204658_-_2018-05-14_19-32-35/11204658_-_2018-05-14_19-32-35.bundle and run: git clone 11204658_-_2018-05-14_19-32-35.bundle Source: https://gist.github.com/11204658 Uploader: benmarwick Upload date: 2018-05-14
Topics: Gist, GitHub, code, software, git
open-archaeo
software

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Cross-Sectional Geometry Tool (CSGR) CSGR Cross-Sectional Geometry tool (CSGR extracts and calculates from long bone cross sections (e.g. mesh derived from CT data) cortical thickness maps, and biomechanically pertinent cross-sectional geometric (CSG) properties. Authors Profico Antonio, Damiano Marchi and Paul O'Higgins To restore the repository download the bundle wget https://archive.org/download/github.com-Arothron-CSGR_-_2018-09-12_11-05-11/Arothron-CSGR_-_2018-09-12_11-05-11.bundle and...
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open-archaeo
software

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Database of roman construction materials, includes shapefiles, primary sources, and archaeological evidence. # Roman-material-database ABSTRACT: The Historic Materials Database is an interactive database of construction materials used in antiquity. This is the first step of my larger PhD project that will enable a wider audience to create 3D and virtual reality (VR) models of historic structures. By helping a user build accurate models, my project will provide new perspectives of historic...
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open-archaeo
software

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GIS Projects for teaching and learning about Computational Archaeology GIS-Projects GIS Projects for teaching and learning about Computational Archaeology Software needed: GRASS GIS QGIS GIMP Video Tutorials: These screen-cast video tutorials cover all the steps to complete the projects below. I include updated versions each year, as some of the details of the software tends to change, but the concepts and basic workflow should remain valid regardless of software version. Play list of 2018...
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open-archaeo
software

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SNP calling and genotyping for damaged DNA AntCaller SNP calling and genotyping for damaged ancient DNA Usage This program is built on Python2.7 and can only be used for SAM/BAM files with MD field under Linux system. Copy three .py files to the directory where SAM/BAM files are stored. Print "python AntCaller-1.1.py -help" for detailed usage information. SNP calling can only be performed after extracting damage information and pileuping reads. Examples for BAM file (Require SAMtools...
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open-archaeo
software

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Android App for remotely controlling camera, weight scale and connecting to database for recording data on archaeology objects Archaeological Artifact Recording - Android App This Android app is designed to facilitate recording weights and colors stored in a Heroku database and downloading images of archaeological artifacts from a remote camera to the device's storage. The user can lookup an artifact by primary key(s)and retrieve all stored information about the object. The app can communicate...
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open-archaeo
software

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This is a LibreOffice Calc spreadsheet designed to help you plan an aerial drone mapping survey mission. DroneSurveyPlanner This is a LibreOffice Calc spreadsheet designed to help you plan an aerial drone mapping survey mission. Beta v0.1 The initial beta release (v.0.1) can be found at the following DOI: How to use: Enter data about your drone, camera, and mission details into the top section. The spreadhsheet calculates the resolution and ground-footprint of each photo as well as transect...
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A Distant Reading of the Day of Archaeology Brainerd-Robinson-Similarity-Coefficient-and-Sampling-Error-Assessment Script for calculating Brainerd-Robinson coefficients based on tabular count or percent data. This script also estimates the probability that a given difference between two samples is the product of sampling error. Brainerd Robinson Coefficient of Similarity: The Brainerd-Robinson (BR) coefficient is a similarity measure that was developed within archaeology specifically for...
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open-archaeo
software

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Modelling and feature detection in palaeoenvironmental time series using additive models Modelling and feature detection in palaeoenvironmental time series using additive models Code and text for manuscript describing my additive modelling approach to modelling palaeoenvironmental time series and detecting periods of significant change in palaeo data. To restore the repository download the bundle wget...
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open-archaeo
software

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Floor plan app using augmented reality. Used for Heritage Structures Lab. ARFloorPlanApp Floor plan app using augmented reality. Used for Heritage Structures Lab.See the Developer Guide for full details. To restore the repository download the bundle wget https://archive.org/download/github.com-carlsun98-ARFloorPlanApp_-_2018-07-27_22-02-36/carlsun98-ARFloorPlanApp_-_2018-07-27_22-02-36.bundle and run: git clone carlsun98-ARFloorPlanApp_-_2018-07-27_22-02-36.bundle Source:...
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open-archaeo
software

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Towards a data standard for paleoanthropology paleocore This is the codebase for the paleocore project. Note regarding settings.py: Local settings are stored in mysite/secrets.py. This file is not included in the GitHub repository for security reasons and must be created during installation. A template for secrets.py is provided at mysite/secrets_template.py. Add your local configuration settings and rename the file secrets.py. Python Environment Django==1.8.4 Pillow==3.0.0 Shapely==1.5.12...
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open-archaeo
software

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Tools for the post-processing of the Markov Chain simulated by any software used for the construction of archeological chronologies To restore the repository download the bundle wget https://archive.org/download/github.com-marieannevibet-ArchaeoPhases_-_2018-07-26_09-58-23/marieannevibet-ArchaeoPhases_-_2018-07-26_09-58-23.bundle and run: git clone marieannevibet-ArchaeoPhases_-_2018-07-26_09-58-23.bundle Source: https://github.com/marieannevibet/ArchaeoPhases Uploader: marieannevibet Upload...
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open-archaeo
by Johanna-Mestorf-Academy
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R Shiny App - Exploration and visualization of SDS datasets (Systematic and digital documentation of stone artefacts) sdsbrowser: sds.ufg.uni-kiel.de What is SDS? SDS ( Systematic and Digital Documentation of Stone Artefacts ) [1] is a recording system for stone artefacts. It was created as an uniform coding and standardized listing system of conventional attributes recorded at lithic inventories to enable well structured, quantitative, and comparative analysis. The variable collection in SDS...
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open-archaeo
software

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Climate Response and Virginia Archaeology: Maps from Different Points of View Climate Response and Virginia Archaeology: Maps from Different Points of View Jolene Smith, Virginia Department of Historic Resources A Paper for the 48th Annual Middle Atlantic Archaeology Conference in Virginia Beach, VA. March 17, 2018. In Geospatial Studies in Middle Atlantic ArchaeologySession Organizer: Yvonne French (Northern Virginia Chapter, Archeological Society of Virginia) Introduction: Expectations for...
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open-archaeo
software

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None QGIS-scripts Random scripts that could be useful for QGIS users... Installing QGIS scripts Simply go to Processing Toolbox -> Scripts -> Tools -> Create new script and paste the code. Or use "Add from file" option (which doesn'talways work) To restore the repository download the bundle wget https://archive.org/download/github.com-zoran-cuckovic-QGIS-scripts_-_2018-07-21_22-11-13/zoran-cuckovic-QGIS-scripts_-_2018-07-21_22-11-13.bundle and run: git clone...
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open-archaeo
software

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R package to help interpreting Correspondence Analysis’ results CAinterprTools vers 0.24 A number of interesting packages are available to perform Correspondence Analysis in R. At the best of my knowledge, however, they lack some tools to help users to eyeball some critical CA aspects (e.g., contribution of rows/cols categories to the principal axes, quality of the display,correlation of rows/cols categories with dimensions, etc). Besides providing those facilities, this package allows...
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open-archaeo
software

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None To restore the repository download the bundle wget https://archive.org/download/github.com-sfsheath-italy-3d-amphitheaters_-_2018-01-21_04-52-13/sfsheath-italy-3d-amphitheaters_-_2018-01-21_04-52-13.bundle and run: git clone sfsheath-italy-3d-amphitheaters_-_2018-01-21_04-52-13.bundle Source: https://github.com/sfsheath/italy-3d-amphitheaters Uploader: sfsheath Upload date: 2018-01-21
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open-archaeo
software

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Tidy Radiocarbon Dating Tools carbon14 The goal of carbon14 is to provide a tidy interface to radiocarbon dating, to promote its inclusion in reproducible manuscripts. Installation You can install carbon14 from github with: ``` r install.packages("devtools") devtools::install_github("paleolimbot/carbon14")``` Example Radiocarbon ages from Long Lake, Nova Scotia, Canada : #> # A tibble: 5 x 4#> sample_id depth age_14C age_error#> #> 1 LL082011-C2-39 94.0 9148...
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open-archaeo
software

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A simple adventure game in Unity2D. Revolves around being an archaeologist exploring some ruin and digging up treasure/fossils. ArchaeologyAdventure A simple adventure game in Unity2D. Revolves around being an archaeologist exploring some ruin and digging up treasure/fossils. To restore the repository download the bundle wget https://archive.org/download/github.com-Camology-ArchaeologyAdventure_-_2018-06-06_19-54-37/Camology-ArchaeologyAdventure_-_2018-06-06_19-54-37.bundle and run: git clone...
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open-archaeo
software

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Consensify method for error reduction in ancient DNA pseudohaploidisation Consensify Documentation for Consensify v0.1 The manuscript accompanying this source is available on BioRxiv: https://www.biorxiv.org/content/early/2018/12/18/498915?rss=1 Axel Barlow and Johanna L. A. Paijmans, December 2018 emails: axel.barlow.ab@gmail.com, paijmans.jla@gmail.com Introduction Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to...
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open-archaeo
software

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A simple qgis plugin that measures the 3d distance between two selected points. Measure 3d - Qgis plugin A simple plugin that measure the 3d distance between two selected points. A field of the attribute table or the geometry (PointZ, PointZM) can be used to get the 3th dimension information. How to use Clone or Download the repository Rename the main folder to measure3d Copy measure3d to Qgis's plugin folder Run Qgis and activate the plugin Screenshot To restore the repository download the...
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open-archaeo
by Integrative-Transcriptomics
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None MADAM - iMproving Ancient Dna AsseMbly Dependencies The following software has to be installed in order for the software to run: jdk7+ bwa: http://bio-bwa.sourceforge.net/ samtools: http://samtools.sourceforge.net/ ClipAndMerge: https://github.com/apeltzer/ClipAndMerge sga: https://github.com/jts/sga SOAPdenovo2: https://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/ MEGAHIT: https://github.com/voutcn/megahit qualimap: http://qualimap.bioinfo.cipf.es/ Note: Clip&Merge is...
Topics: GitHub, code, software, git